Here are the secondary structure predictions predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Threonines at residues 41 and 43 are highly predicted to be part of a sheet. However, the Threonines at residues 68 and 114 are not predicted to be anything!
_____________________________________________________

More details in the blogpost for this puzzle: http://fold.it/portal/node/995344

is cys bonding being given extra points?

Thanks for bringing this up, MikeCassidy!
(I'm glad to see that my last sentence in this blogpost worked so fast :-)

We did NOT turn on the Disulfide Count Score Filter on this puzzle, but it can easily be added if needed.

I have asked the scientists at the Worcester Polytechnic Institute who are working on this unsolved protein for their expertise on the matter.

Thank you again for asking this!